A computerized timekeeping system that was supposed to save the city’s social-service agency millions of dollars ended up costing twice as much as planned and saved no money, City Comptroller Bill Thompson said yesterday.

An audit by Thompson’s office found that the AutoTime paperless system used by the Human Resource Administration is fraught with problems and still incomplete after seven years of use.

From overtime calculations to field work hours to holiday compensations, the system still is unable to work.

“HRA spent over $24.8 million, more than double the initial contract amount of $9.6 million, for an incomplete timekeeping system,” the comptroller said.

“Our report also shows that none of the estimated $15.7 million in savings claimed by HRA will be realized. The city can ill afford this type of waste, particularly during these tight budgetary times,” Thompson added

The system is in place at 120 HRA work sites.

AutoTime was created by Davisco Inc. to help HRA reduce the cost of timekeeping, eliminate paperwork, reduce errors in employee records and allow them to transmit directly the city’s payroll system.

Thompson said that despite HRA looking at the contract five times, they never followed through on getting an outside quality-assurance specialist to work out the kinks.

A spokesman for HRA, Carl Strange, did not dispute the comptroller’s findings.

He would only say the system works and “is used by over 14,000 employees here at HRA and it helps us increase accuracy, efficiency and productivity.”